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Lloret-Villas A, Daudin R, Le Novère N. "Big Data" in neuroscience: open door to a more comprehensive and translational research [Internet]. Big Data Analytics 2016;1:5.Available from:
Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 2006;34(Database issue):D689-91.
Chelliah V, Juty N, Laibe C, Hermjakob H, Le Novère N. BioModels Database: a public repository for sharing models of biological processes. In: Encyclopedia of Computational Neuroscience. New York Heidelberg Dordrecht London : Springer-Verlag; 2015
Chelliah V, Laibe C, Le Novère N. BioModels Database: a repository of mathematical models of biological processes. Methods Mol Biol 2013;1021:189-99.
Chelliah V, Laibe C, Le Novère N. BioModels Database, A Repository of Mathematical Models of Biological Processes. In: Encyclopedia of Systems Biology. Springer; 2013
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 2010;4:92.
Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne S, Hermjakob H, Le Novère N, Laibe C, Chelliah V. BioModels Database: content, features, functionality and use. CPT: Pharmacometrics & Systems Pharmacology 2015;2(4):1-14.
Glont M, Nguyen TV, Graesslin M, Raza A, Schramm J, Wimalaratne SM, Kothamachu VB, Rodriguez N, Swat M, Eils J, Eils R, Laibe C, Malik-Sheriff R, Chelliah V, Le Novère N, Hermjakob H. BioModels: Expanding horizons to include more modelling approaches and formats [Internet]. Nucleic Acids Research 2018;46(D1):D1248-D1253.Available from:
Wimalaratne SM, Grenon P, Hermjakob H, Le Novère N, Laibe C. BioModels linked dataset. BMC Syst Biol 2014;8:91.
Le Novère N. BioModels. net, tools and resources to support Computational Systems Biology. In: 4th Workshop on Computation of Biochemical Pathways and Genetic Networks. 2005 p. 69–74.
Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan K, Pettit J-B, Rodriguez N, Schubert M, Wimalaratne S, Zhou Y, Hermjakob H, Le Novère N, Laibe C. BioModels: ten year anniversary [Internet]. Nucleic Acids Research 2015;Available from:
Li C, Courtot M, Le Novère N, Laibe C. Web Services, a free and integrated toolkit for computational modelling software. Brief Bioinform 2010;11(3):270-7.
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung K-H, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD. The BioPAX community standard for pathway data sharing. Nat Biotechnol 2010;28(9):935-42.
Gambardella L, McManus SA, Moignard V, Sebukhan D, Delaune A, Andrews S, Bernard WG, Morisson MA, Riley PR, Gottgens B, Le Novère NGambardell, Sinha S. BNC1 regulates cell heterogeneity in human pluripotent stem cell derived-epicardium. Development 2019;146:dev174441.
Myers CJ, Bader G, Gleeson P, Golebiewski M, Hucka M, Le Novère N, Nickerson DP, Schreiber F, Waltemath D. A brief history of COMBINE. Winter Simulation Conference 2017 2017;:884-895.
Tolle DP, Le Novère N. Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP. BMC Syst Biol 2010;4:25.
Li L, Stefan MI, Le Novère N. Calcium input frequency, duration and amplitude differentially modulate the relative activation of calcineurin and CaMKII. PLoS One 2012;7(9):e43810.
Schilstra MJ, Li L, Matthews J, Finney A, Hucka M, Le Novère N. CellML2SBML: conversion of CellML into SBML. Bioinformatics 2006;22(8):1018-20.
Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project [Internet]. BMC Systems Biology 2014;15:369 .Available from:
Bergmann FT, Rodriguez N, Le Novère N. COMBINE archive specification Version 1. Journal of Integrative Bioinformatics 2015;12(2):261.
Beal J, Nguyen T, Gorochowski TE, Goñi-Moreno A, Scott-Brown J, McLaughlin JAlastair, Madsen C, Aleritsch B, Bartley B, Bhakta S, Bissell M, Castillo-Hair S, Clancy K, Luna A, Le Novère N, Palchick Z, Pocock M, Sauro H, Sexton J, Tabor J, Voigt C, Zundel Z, Myers C, Wipat A. Communicating Structure and Function in Synthetic Biology Diagrams [Internet]. ACS Synthetic Biology 2019;8(8):1818-1825.Available from:
Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Goryanin I, Gudmundsson S, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, Van Beek H, Weichart D, Nielsen JB, Westerhoff HV, Kell DB, Mendes P, Palsson BØ. A community-driven global reconstruction of human metabolism. Nat Biotechnol 2013;31(5):419-425.
Ostaszewski M, Gebel S, Kuperstein I, Mazein A, Zinovyev A, Dogrusoz U, Hasenauer J, Fleming R, Le Novère N, Gawron P, Ligon T, Niarakis A, Nickerson D, Weindl D, Balling R, Barillot E, Auffray C, Schneider R. Community-driven roadmap for integrated disease maps [Internet]. Briefings in Bioinformatics 2018;Available from:
Guerlet G, Taly A, Prado de Carvalho L, Martz A, Jiang R, Specht A, Le Novère N, Grutter T. Comparative models of P2X2 receptor support inter-subunit ATP-binding sites. Biochem Biophys Res Commun 2008;375(3):405-9.
Stefan MI, Edelstein SJ, Le Novère N. Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters. BMC Syst Biol 2009;3:68.
Changeux J-P, Edelstein SJ. Conformational selection or induced fit? 50 years of debate resolved. F1000 Biol Rep 2011;3:19.
Changeux J-P, Edelstein S. Conformational selection or induced fit? 50 years of debate resolved. F1000 Biol Rep 2011;3:19.
Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga YK, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 2008;26(10):1155-60.
Henkel R, Le Novère N, Wolkenhauer O, Waltemath D. Considerations of graph-based concepts to manage of computational biology models and associated simulations. INFORMATIK 2012 2012;
Alcasabas AA, de Clare M, Pir P, Oliver SG. Control analysis of the eukaryotic cell cycle using gene copy-number series in yeast tetraploids. BMC Genomics 2013;14:744.
Juty N, Laibe C, Le Novère N. Controlled annotations for systems biology. Methods Mol Biol 2013;1021:227-45.
Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N. Controlled vocabularies and semantics in systems biology. Mol Syst Biol 2011;7:543.
Stefan MI, Le Novère N. Cooperative binding. PLoS Computational Biology 2013;9(6)
Naldi A, Monteiro PT, Müssel C, Albert R, Barberis M, Calzone L, Chasapi A, Cokelaer T, Crespo I, Dorier J, Dräger A, Hernandez C, Hucka M, de Jong H, Keating SM, Klamt S, Klarner H, Laubenbacher R, Le Novère N, Niknejad A, Rodriguez N, Siebert H, Stoll G, Zañudo JGT, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C. Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinformatics 2015;31(7):1154-1159.
Edelstein SJ, Le Novère N. Cooperativity of allosteric receptors. Journal of Molecular Biology 2013;425(9): 1424-1432.
Fernandez E, Schiappa R, Girault J-A, Le Novère N. DARPP-32 is a robust integrator of dopamine and glutamate signals. PLoS Comput Biol 2006;2(12):e176.
Le Novère N, Li L, Girault J-A. DARPP-32: molecular integration of phosphorylation potential. Cell Mol Life Sci 2008;65(14):2125-7.
Chelliah V, Endler L, Juty N, Laibe C, Li C, Rodriguez N, Le Novère N. Data Integration and Semantic Enrichment of Systems Biology Models and Simulations. In: 6th International workshop Data Integration in the Life Sciences. Springer; 2009 p. 5–15.
Juty N, Le Novère N, Hermjakob H, Laibe C. Delivering “Cool URIs” that do not change [Internet]. In: SWAT4LS 2012. 2012Available from:
Poitevin F, Edelstein SJ. Derivation of the Crick-Wyman equation for allosteric proteins defining the difference between the number of binding sites and the Hill coefficient. Journal Of Molecular Biology 2013;425(9):1497–1499.
Endler L, Rodriguez N, Juty N, Chelliah V, Laibe C, Li C, Le Novère N. Designing and encoding models for synthetic biology. J R Soc Interface 2009;6 Suppl 4:S405-17.
Ebrahim A, almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RMT, Fong SS, Hatzimanakis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SYup, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Niels LK, Nogales J, Noronha A, Pal C, Palsson BØ, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I. Do Genome-scale Models Need Exact Solvers or Clearer Standards?. Molecular Systems Biology 2015;11(10)
Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling M, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Le Novère N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D. Harmonizing semantic annotations for computational models in biology [Internet]. BiorXiv 2018;:246470 .Available from:
Dumontier M, Gray AJG, Marshall SM, Alexiev V, Ansell P, Bader GD, Baran J, Bolleman J, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz E, Gonzalez-Beltran A, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayam T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall C, Rietveld L, Wimalaratne SM, Yamaguchi A. The health care and life sciences community profile for dataset descriptions. PeerJ 2016;4:e2331.
Nguyen A, Guedán A, Mousnier A, Swieboda D, Zhang Q, Horkai D, Le Novère N, Solari R, Wakelam MJO. Host lipidome analysis during rhinovirus replication in human bronchial epithelial cells identifies potential therapeutic targets. [Internet]. Journal of Lipid Research 2018;Available from:
Bargehr J, Ong LP, Colzani M, Davaapil H, Hofsteen P, Bhandari, iv S, Gambardella L, Le Novère N, Iyer D, Sampaziotis F, Weinberger F, Bertero A, Leonard A, Bernard WG, Martinson A, Figg N, Regnier M, Bennett MR, Murry CE, Sinha S. Human embryonic stem cell-derived epicardial cells augment cardiomyocyte-driven heart regeneration [Internet]. Nature Biotechnology 2019;37:895–906.Available from:
McMurry J, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Hastings J, Haendel MA, Hermjakob H, Hériché J-K, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Mungall CJ, Rocca-Serra P, Sansone S-A, Sariyar M, Snoep JL, Stanford NJ, Soiland-Reyes S, Swainston N, Washington N, Williams AR, Wolstencroft K, Goble C, Parkinson H. Identifiers for the 21st century: How to design, provision, and reuse identifiers to maximize data utility and impact of life science data [Internet]. PLoS Biology 2017;15(6):e2001414.Available from:
Juty N, Le Novère N, Laibe C. and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res 2012;40(Database issue):D580-6.
Laibe C, Wimalaratne S, Juty N, Le Novère N, Hermjakob H. integration tool for heterogeneous datasets. 10th International workshop Data Integration in the Life Sciences 2014;
Villas ALloret i, Varusai TM, Juty N, Laibe C, Le Novère N, Hermjakob H, Chelliah V. The impact of mathematical modeling in understanding the mechanisms underlying neurodegeneration: evolving dimensions and future directions [Internet]. CPT: Pharmacometrics & Systems Pharmacology 2017;Available from:
Ajmera I, Swat M, Laibe C, Le Novère N, Chelliah V. The impact of mathematical modeling on the understanding of diabetes and related complications. CPT: Pharmacometrics & Systems Pharmacology 2013;2:e54.
Adams RR, Tsorman N, Stratford K, Akman OE, Gilmore S, Juty N, Le Novère N, Millar AJ, Millar AJ. The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models. J Biol Rhythms 2012;27(4):328-32.
Mattioni M, Le Novère N. Integration of biochemical and electrical signaling - multiscale model of the medium spiny neuron of the striatum. PLoS ONE 2013;8(7):e66811.
Prevost MS, Moraga-Cid G, Van Renterghem C, Edelstein SJ, Changeux J-P, Corringer P-J. Intermediate closed state for glycine receptor function revealed by cysteine cross-linking. Proc Natl Acad Sci U S A 2013;110(42):17113-8.
Shapiro BE, Finney A, Hucka M, Bornstein B, Funahashi A, Jouraku A, Keating SM, Novère N, Matthews J, Schilstra MJ. Introduction to Systems Biology. Humana Press; 2007 p. 395–421.
Pir P, Le Novère N. Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine. In: Methods Molecular Biology: Systems Medicine. Springer; 2016 p. 331-350.
Le Novère N, Hucka M, Anwar N, Bader GD, Demir E, Moodie S, Sorokin A. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). Stand Genomic Sci 2011;5(2):230-42.
Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Lucian S, Zhang F, Eric B. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Standards in Genomic Sciences 2013;9
Kettner C, Field D, Sansone S, Taylor C, Aerts J, Binns N, Blake A, Britten CM, Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL. Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations” (MIBBI) workshop. Standards in Genomic Sciences 2010;3:259-266.
Dumousseau M, Rodriguez N, Juty N, Le Novère N. MELTING, a flexible platform to predict the melting temperatures of nucleic acids. BMC Bioinformatics 2012;13:101.
Lieven C, Beber MEmanuel, Olivier BG, Bergmann FT, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BElisabeth, Edirisinghe JN, Fleming RMT, Garcia-Jimenez B, van Helvoirt W, Henry C, Hermjakob H, Herrgård MJ, Kim HUk, King Z, Koehorst JJan, Klamt S, Klipp E, Lakshmanan M, Le Novère N, Lee D-Y, Lee SYup, Lee S, Lewis NE, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk J, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Resendis O, Palsson B, Papin JA, Patil KRaosaheb, Price ND, Richelle A, Rocha I, Schaap P, Sheriff RSMalik, Shoaie S, Sonnenschein N, Teusink B, Vilaca P, Vik JOlav, Wodke JA, Xavier JC, Yuan Q, Zakhartsev M, Cheng Z. Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite. BiorXiv 2018;
Tolle DP, Le Novère N. Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes. BMC Syst Biol 2010;4:24.
Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N. Minimum Information About a Simulation Experiment (MIASE). PLoS Comput Biol 2011;7(4):e1001122.
Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, Wanner BL. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 2005;23(12):1509-15.
Laibe C, Le Novère N. MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. BMC Syst Biol 2007;1:58.
Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JEG, Paton NW, Westerhoff HV, Kell DB, Mendes P. A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Lett 2013;587(17):2832-41.
Le Novère N. Model storage, exchange and integration. BMC Neurosci 2006;7 Suppl 1:S11.
Wittig MA, Hastings J, Rodriguez N, Joshi CJ, Hattwell JPN, Ebert PR, Van Weeghel M, Gao AW, Wakelam MJO, Houtkooper RH, Mains A, Le Novère N, Sadykoff S, Schroeder F, Lewis N, Schirra H-J, Kaleta C, Casanueva O. Modeling meets Metabolomics – The WormJam Consensus Model as basis for Metabolic Studies in the model organism Caenorhabditis elegans [Internet]. Frontiers in Molecular Biosciences 2018;5:96.Available from:
Lai M, Brun D, Edelstein S, Le Novère N. Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions [Internet]. PLoS Computational Biology 2015;11(1):e1004063.Available from:
Le Novère N, Donizelli M. The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet). BMC Bioinformatics 2004;5:174.
Hastings J, Mains A, Virk B, Rodriguez N, Murdoch S, Pearce J, Bergmann S, Le Novère N, Casanueva O. Multi-omics and genome-scale modeling reveal a metabolic shift during C. elegans aging [Internet]. Frontiers in Molecular Biosciences 2019;Available from:
Li L, Lai M, Cole S, Le Novère N, Edelstein S. Neurogranin Stimulates Ca2+/calmodulin-dependent Kinase II by Inhibiting Calcineurin at Specific Calcium Spike Frequencies. BiorXiv 2019;2019/1/1
Li L, Lai M, Cole S, Le Novère N, Edelstein SJ. Neurogranin Stimulates Ca2+/Calmodulin-dependent Kinase II by Suppressing Calcineurin Activity at Specific Calcium Spike Frequencies. PLoS Computational Biology In Press;
Le Novère N. Neurological disease: are systems approaches the way forward?. Pharmacopsychiatry 2008;41 Suppl 1:S28-31.
Mattioni M, Cohen U, Le Novère N. Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON. Front Neuroinform 2012;6:20.
Taly A, Delarue M, Grutter T, Nilges M, Le Novère N, Corringer P-J, Changeux J-P. Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism. Biophys J 2005;88(6):3954-65.
Edelstein SJ. A Novel Equation for Cooperativity of the Allosteric State Function. Journal of Molecular Biology 2014;426:39-42.
Schapira AHV, Bezard E, Brotchie J, Calon F, Collingridge GL, Ferger B, Hengerer B, Hirsch E, Jenner P, Le Novère N, Obeso JA, Schwarzschild MA, Spampinato U, Davidai G. Novel pharmacological targets for the treatment of Parkinson's disease. Nat Rev Drug Discov 2006;5(10):845-54.
Tolle DP, Le Novère N. Particle-based stochastic simulation in systems biology. Current Bioinformatics 2006;1:315–320.
Le Novère N, Tolle D. Particle-based stochastic simulations. In: Proceedings of the 4th Workshop on Computation of Biochemical Pathways and Genetic Networks. Logos; 2005 p. 41-45.
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Drager A, Le Novère N. Path2Models: Large-scale generation of computational models from biochemical pathway map [Internet]. BMC Systems Biology 2013;7:116.Available from:
Kiselev VY, Juvin V, Mouhannad M, Luscombe NM, Hawkins P, Le Novère N, Stephens LR. Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop [Internet]. Nucleic Acids Research 2015;43(20): 9663-9679.Available from:
Swat MJ, Moodie S, Wimalaratne SM, Kristensen NRode, Lavielle M, Mari A, Magni P, Bizzoto R, Smith M, Comets E, Sarr C, Terranova N, Blaudez E, Chan P, Chard J, Chenel M, Edwards D, Franklin C, Giorgina T, Glont M, Girard P, Grenon P, Harling K, Hooker AC, Kaye R, Keizer R, Kloft C, Kobash N, Laibe C, Laveille C, Mentre F, Mezzalana E, Munafo A, Nordgren R, Nyberg HB, Para-Guillen ZP, Pasotti L, Plan E, Ribba B, Smith G, Trocóniz IF, Yvon F, Harnisch L, Karlsson M, Hermjakob H, Le Novère N. Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development. CPT: Pharmacometrics & Systems Pharmacology 2015;6:316-319.
Waltemath D, Wolkenhauer O, Le Novère N, Dumontier M. Possibilities for Integrating Model-related Data in Computational Biology [Internet]. 9th International workshop Data Integration in the Life Sciences 2013;Available from:
Dikicioglu D, Pir P, Oliver SG. Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory. Biotechnol J 2013;8(9):1017-34.
Knight-Schrijver V, Chelliah V, Cucurull-Sanchez L, Le Novère N. The promises of quantitative systems pharmacology modelling for drug development [Internet]. Computational and Structural Biotechnology Journal 2016;14:363–370.Available from:
Taylor CF, Field D, Sansone S-A, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz P-A, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon A-M, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 2008;26(8):889-96.
Hucka M, Nickerson DPhillip, Bader G, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJohn, Schreiber F, Waltemath D, Le Novère N. Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative [Internet]. Frontiers in Bioengineering and Biotechnology 2015;3:19.Available from:
Malek M, Kielkowska A, Chessa T, Anderson KE, Barneda D, Pir P, Nakanishi H, Eguchi S, Koizumi A, Sasaki J, Juvin V, Kiselev VYu, Niewczas I, Gray A, Valayer A, Spensberger D, Imbert M, Felisbino S, Habuchi T, Beinke S, Cosulich S, Le Novère N, Sasaki T, Hawkins P, Clark J, Stephens LR. PTEN regulates PI(3,4)P2 signalling downstream of class I PI3K [Internet]. Molecular Cell 2017;68(3):566–580.Available from:
Waltemath D, Swainston N, Lister A, Bergmann F, Henkel R, Hoops S, Hucka M, Juty N, Keating S, Knuepfer C, others. SBML Level 3 Package Proposal: Annot. Nature Precedings 2011;
Shapiro BE, Finney A, Hucka M, Borstein B, Funahashi A, Jouraki A, Keating SM, Le Novère N, Matthews JA, Schilstra MJ. SBML Models and MathSBML. In: Choi S. Humana Press, USA; 2007
Chaouiya C, Berenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, çalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Systems Biology 2013;7(1):135.
Dräger A, Planatscher H, Wouamba DMotsou, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A. SBML2L(A)T(E)X: conversion of SBML files into human-readable reports. Bioinformatics 2009;25(11):1455-6.
Rodriguez N, Donizelli M, Le Novère N. SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML). BMC Bioinformatics 2007;8:79.
Quinn JYuan, Cox, III RSidney, Adler A, Beal J, Bhatia S, Cai Y, Chen J, Clancy K, Galdzicki M, Hillson NJ, Le Novère N, Maheshwari A, McLaughlin JAlastair, Myers C, P U, Pocock M, Rodriguez C, Soldatova L, Stan G-B, Swainston N, Sauro HM, Wipat A. SBOL Visual: Standard Schematics for Synthetic Genetic Constructs. PLoS Biology 2015;13(12):e1002310.
Pezze PDalle, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks [Internet]. BMC Systems Biology 2017;11:46.Available from:
Baldi BF, Hoyer C, Le Novère N. Schizophrenic: forever young?. Genome Med 2010;2(5):32.
Köhn D, Le Novere N. SED-ML–an XML format for the implementation of the MIASE guidelines. In: Heiner M, Uhrmacher AMProceedings of the 6th conference on Computational Methods in Systems Biology. Springer Berlin/Heidelberg; 2008 p. 176–190.
Boras V, Fucic A, Virag M, Gabric D, Blivajs I, Tomasovic-Longaric C, Rakusic Z, Bisof V, Le Novère N, Vrdoljak DV. Significance of stroma in biology of oral squamous cell carcinoma. Tumori 2018;104(1):9-14.
Le Novère N, Finney A. A simple scheme for annotating SBML with references to controlled vocabularies and database entries [Internet]. 2005;Available from: lenov/PUBLIS/Lenov2005d.pdf
Waltemath D, Le Novère N. Simulation Experiment Description Markup Language (SED-ML). In: Encyclopedia of computational neuroscience. 2013
Bergmann FT, Cooper J, Le Novère N, Nickerson DP, Waltemath D. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2. Journal of Integrative Bioinformatics 2015;12(2):262.
Bergmann FT, Cooper J, König M, Moraru I, Nickerson D, Le Novère N, Olivier BG, Sahle S, Lucian S, Waltemath D. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). Journal of Integrative Bioinformatics 2018;15(1):20170086.
Waltemath D, Bergmann FT, Adams R, Le Novère N. Simulation Experiment Description Markup Language (SED-ML): Level 1 Version 1. Nat Precedings 2011;
van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F. Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics 2012;28(15):2016-21.
Hucka M, Le Novère N. Software that goes with the flow in systems biology. BMC Biol 2010;8:140.
Wimalaratne SM, Bolleman J, Juty N, Katayam T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C. SPARQL-enabled identifier conversion with Bioinformatics 2015;
Schreiber F, Bader GD, Golebiewski M, Hucka M, Kornmeier B, Le Novère N, Myers CJ, Nickerson DP, Sommer B, Waltemath D, Weise S. Specifications of Standards in Systems and Synthetic Biology. Journal of Integrative Bioinformatics 2015;12(2):258.
Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Le Novère N, Myers C, Nickerson D, Sommer B, Waltemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. Journal of Integrative Bioinformatics 2018;15(1):20180013.
Stefan MI, Marshall DP, Le Novère N. Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKII. PLoS One 2012;7(1):e29406.
Knüpfer C, Beckstein C, Dittrich P, Le Novère N. Structure, function, and behaviour of computational models in systems biology. BMC Syst Biol 2013;7:43.
Keating SM, Le Novère N. Supporting SBML as a model exchange format in software applications. Methods Mol Biol 2013;1021:201-25.
von Eichborn J, Dunkel M, Gohlke B, Preissner S, Hoffmann M, Bauer J, Armstrong JD, Schaefer M, Andrade M, Le Novère M, Croning M, Grant SGN, van Nierop P, Smit AB, Preissner R. SynSysNet: Integration of experimental data on synaptic protein-protein interactions with drug-target relations [Internet]. Nucleic Acids Res. 2013;41(D1):D834-D840.Available from:
Cox RS, Madsen C, McLaughlin J, Nguyen T, Roehner N, Bartley B, Bhatia S, Bissell M, Clancy K, Gorochowski T, Grünberg R, Luna A, Le Novère N, Pocock M, Sauro H, Sexton JT, Stan G-B, Tabor JJ, Voigt CA, Zundel Z, Myers C, Beal J, Wipat A. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0. Journal of Integrative Bioinformatics 2018;15:20170074.
Madsen C, Moreno AGoni, Palchick Z, P U, Roehner N, Bartley B, Bhatia S, Bhakta S, Bissel M, Clancy K, Cox RSidney, Gorochowski T, Grünberg R, Luna A, McLaughlin J, Nguyen T, Le Novère N, Pocock M, Sauro H, Scott-Brown J, Sexton JT, Stan G-B, Tabor JJ, Voigt CA, Zundel Z, Myers C, Beal J, Wipat A. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1 [Internet]. Journal of Integrative Bioinformatics 2019;:Online advance publication.Available from:
Wolkenhauer O, Fell D, De Meyts P, Blüthgen N, Herzel H, Le Novère N, Höfer T, Schürrle K, van Leeuwen I. SysBioMed report: advancing systems biology for medical applications. IET Syst Biol 2009;3(3):131-6.
Rodriguez N, Pettit J-B, Pezze PDalle, Li L, Henry A, van Iersel MP, Jalowicki G, Kutmon M, Natarajan KN, Tolnay D, Stefan MI, Evelo CT, Le Novère N. The Systems Biology Format Converter. BMC Bioinformatics 2016;17:154.
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villeger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. The Systems Biology Graphical Notation. Nat Biotechnol 2009;27(8):735-41.
Mi H, Schreiber F, Le Novére N, Moodie S, Sorokin A. Systems biology graphical notation: Activity flow language level 1. Nature Precedings 2009;
Mi H, Schreiber F, Moodie SL, Czauderna T, Demir E, Haw R, Luna A, Le Novère N, Sorokin A, Villéger AC. Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2. Journal of Integrative Bioinformatics 2015;12:266.
Sorokin A, Le Novère N, Luna A, Czauderna T, Demir E, Haw R, Mi H, Moodie SL, Schreiber F, Villéger AC. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. Journal of Integrative Bioinformatics 2015;12(2):264.